David, The results from using version 3.3.1 is different from version 3.3.2.
In version 3.3.1, adding "SOL OL 0" and executing "genbox -cs tip5p.gro -box 1 1 1" created a box with 37 SOL molecules but the density is too high at 3072.87 g/L. In version 3.3.2, adding "SOL OL 0" did not work. However, I added "SOL LP 0" to the end of vdwradii.dat and the resulting water box contained 37 SOL molecules. The density is incorrect at 2582.79 g/l. This box contains six more SOL molecules compared to a box created with TIP4P water. JW On 10/7/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > JW Feng wrote: > > Hello, > > > > I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, > > TIP4P and TIP5P water with " > > genbox -cs <water model>.gro -box 1 1 1". The TIP5P box contains half > > the number of water molecules compared to TIP4P and SPC. > > SPC: 33 SOL molecules, density=987.205 (g/l) > > TIP4P: 31 SOL molecules > > TIP5P: 15 SOL molecules > > > > Can anyone please explain this? How do I get genbox to create a box > > with the right number of TIP5P water molecules. > > Thanks, > > > > JW > > > It is because of the name of the lone pairs (OL) which is interpreted as > an oxygen atom. You can add OL in vdwradii.dat with radius 0 and try > again. Please report whether it works, then I will fix it in further > releases. > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
